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Yes, upset stomach can be a side effect. You should probably talk to your Dr or pharmacist about how to deal with it. Taking it with food may help. Here is what the medication guide states: Tears (perforation) in the stomach or intestines.

Tell your healthcare provider if you have had diverticulitis (inflammation in parts of the large intestine) or ulcers in your stomach or intestines. Some people taking Xeljanz get tears in their stomach or intestine. This happens most often in people who also take nonsteroidal anti-inflammatory drugs (NSAIDs), corticosteroids, or methotrexate.Tell your healthcare provider right away if you have fever and stomach-area pain that does not go away, and a change in your bowel habits.